Contacts of the helix formed by residues 10 - 23 (chain B) in PDB entry 6ACQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B GLY* 3.4 3.6 + - - -
9B ALA* 1.3 78.0 - - - +
11B THR* 1.3 66.7 + - - -
12B MET 3.4 1.6 - - - -
13B GLY 3.9 3.1 - - - +
14B SER* 2.7 28.1 + - - -
31B ASP* 4.7 0.2 + - - -
39B ARG* 3.8 18.8 - - - +
43B PHE* 5.6 0.4 - - - -
87B ALA 5.5 2.7 + - - -
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Residues in contact with THR 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLY* 1.3 70.4 - - - +
12B MET* 1.3 65.9 + - + +
14B SER* 3.8 1.6 - - - -
15B GLY* 3.0 21.1 + - - -
39B ARG* 5.1 3.2 + - - +
43B PHE* 4.0 29.9 - - + -
141B ASN* 3.6 26.4 - - - +
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Residues in contact with MET 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLY 3.4 0.4 - - - -
11B THR* 1.3 80.6 - - - +
13B GLY* 1.3 58.3 + - - +
15B GLY* 3.4 2.5 + - - -
16B ILE* 2.9 44.8 + - + +
87B ALA* 4.8 5.2 - - + +
115B ASN* 4.0 22.7 - - - +
139B PHE* 3.5 41.3 - - + +
140B PHE 4.4 0.4 - - - +
141B ASN* 3.7 39.3 - - - +
143B ALA* 4.0 10.8 - - + -
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Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.4 20.0 - - - +
8B GLY 3.3 24.9 - - - -
10B GLY* 3.4 5.1 + - - +
11B THR 3.3 0.4 - - - -
12B MET* 1.3 78.6 - - - +
14B SER* 1.3 63.6 + - - +
16B ILE* 3.4 1.8 + - - -
17B ALA* 3.2 19.2 + - - +
29B LEU* 4.0 2.0 - - - +
87B ALA* 3.9 14.3 + - - +
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Residues in contact with SER 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLY 4.3 1.2 + - - -
9B ALA* 3.2 14.9 + - - +
10B GLY 2.7 22.4 + - - -
11B THR 3.8 0.2 - - - -
13B GLY* 1.3 75.0 - - - +
15B GLY* 1.3 58.2 + - - +
17B ALA* 3.2 5.9 + - - +
18B GLN* 2.9 29.5 + - - +
29B LEU* 4.7 4.5 - - - -
40B GLY* 3.2 15.9 - - - -
43B PHE* 3.5 24.8 - - - -
44B ILE* 3.6 21.7 - - - +
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Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR 3.0 12.0 + - - -
12B MET 3.7 3.8 - - - -
14B SER* 1.3 79.7 - - - +
16B ILE* 1.3 56.0 + - - +
18B GLN* 3.4 6.1 + - - +
19B ALA* 3.0 24.4 + - - +
43B PHE* 4.6 6.2 - - - -
143B ALA* 3.6 12.6 - - - +
144B PRO* 3.5 26.3 - - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.1 9.0 - - + -
12B MET* 2.9 39.5 + - + +
13B GLY* 3.9 7.9 - - - +
14B SER 3.2 0.6 - - - -
15B GLY* 1.3 74.3 - - - +
17B ALA* 1.3 64.4 + - - +
19B ALA* 3.4 5.0 + - - +
20B PHE* 3.0 53.3 + - + -
85B ILE* 3.8 21.8 - - + -
87B ALA* 4.6 7.0 - - + -
115B ASN* 4.4 10.5 - - - -
139B PHE* 3.8 31.6 - - + -
143B ALA* 3.8 15.5 - - + -
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.2 7.4 - - + +
13B GLY 3.2 10.6 + - - +
14B SER 3.2 7.8 + - - +
16B ILE* 1.3 76.7 - - - +
18B GLN* 1.3 62.2 + - - +
20B PHE* 3.3 3.0 + - - +
21B ALA* 2.9 32.7 + - - +
27B VAL* 3.7 27.1 - - + +
29B LEU* 4.1 16.6 - - + -
44B ILE* 4.5 7.9 - - + -
69B ILE* 4.2 6.0 - - + +
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Residues in contact with GLN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B SER 2.9 15.7 + - - +
15B GLY* 3.5 7.3 - - - +
17B ALA* 1.3 77.9 - - - +
19B ALA* 1.3 55.6 + - - +
21B ALA* 3.9 0.3 - - - +
22B ALA* 2.8 36.8 + - + +
44B ILE* 3.5 27.7 - - + +
47B ASN* 3.3 39.7 + - - +
48B LEU* 3.8 23.4 - - + +
51B LEU* 4.6 9.7 - - - +
65B ILE* 4.6 1.7 - - + +
69B ILE* 4.4 10.1 - - - -
144B PRO* 3.8 24.3 - - + +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY 3.0 16.6 + - - +
16B ILE* 3.7 8.7 - - - +
17B ALA 3.2 0.4 - - - -
18B GLN* 1.3 78.0 - - - +
20B PHE* 1.3 59.9 + - + +
22B ALA* 3.9 5.1 + - - +
23B LYS* 3.6 25.8 + - - +
139B PHE* 5.5 2.0 - - + -
143B ALA* 4.2 6.7 - - + +
144B PRO* 4.1 20.4 - - + +
172B ILE* 4.2 11.8 - - + +
174B LYS* 4.3 14.8 - - - -
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 3.7 26.9 - - + -
6B VAL* 5.2 0.4 - - + -
16B ILE* 3.0 32.9 + - + +
17B ALA* 3.8 1.3 - - - +
18B GLN 3.2 0.2 - - - -
19B ALA* 1.3 76.9 - - - +
21B ALA* 1.3 66.7 + - - +
23B LYS 3.1 7.6 + - - -
25B PHE* 3.0 47.3 + + + -
27B VAL* 3.6 18.6 - - + -
83B LEU* 4.2 9.9 - - + -
85B ILE* 3.5 31.4 - - + -
137B MET* 4.5 7.2 - - + -
139B PHE* 4.2 3.8 - + - -
168B THR* 3.9 20.6 - - - -
172B ILE* 3.8 32.1 - - + -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA 2.9 17.8 + - - +
18B GLN 3.9 1.3 - - - +
20B PHE* 1.3 77.9 - - - +
22B ALA* 1.3 60.2 + - - +
24B GLY 3.0 3.6 + - - -
25B PHE 3.6 13.7 - - - +
27B VAL* 3.8 4.7 - - + +
65B ILE* 3.8 16.4 - - + +
68B ARG* 2.9 31.6 + - + -
69B ILE* 3.4 31.9 - - + -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLN* 2.8 22.2 + - + +
19B ALA* 4.0 7.9 - - - +
21B ALA* 1.3 78.6 - - - +
23B LYS* 1.3 72.3 + - - +
24B GLY 3.3 0.8 + - - -
48B LEU* 5.8 1.8 - - + -
65B ILE* 3.9 28.1 - - + +
68B ARG* 4.3 5.2 + - - -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-6B LEU 3.4 12.2 - - - +
-4B PRO* 3.6 15.9 - - + +
19B ALA 3.6 14.4 + - - +
20B PHE 3.1 6.5 + - - +
21B ALA 3.1 1.0 - - - -
22B ALA* 1.3 91.4 + - - +
24B GLY* 1.3 57.2 + - - +
25B PHE* 3.7 2.2 - - + -
171B ALA 4.0 8.3 - - - +
172B ILE* 3.6 49.1 + - + +
173B GLY* 4.5 6.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il